Mycobacterium bovis, the causative agent of bovine tuberculosis, has no known geographical boundaries. M. bovis infection occurs in diverse groups of animals, which include farm animals of economic importance, wildlife, and humans (1,16,17,31). Despite these ominous features of M. bovis, to date there have been only projected global estimates of the disease burden. There has been no international effort to determine the actual disease burden, owing to the nonavailability of a reliable user-friendly technology for early detection of M. bovis in clinical samples. Bovine tuberculosis has been on the increase in developed countries and continues to occur in developing countries (6, 14, 16). In Africa, approximately 85% of cattle and 82% of the human population live in areas where the disease is prevalent (6, 26). There are limited reports from India (24, 27, 38, 40) and from underdeveloped countries (6, 16) relating to the prevalence of and infection with M. bovis in cattle. Detection of M. bovis in bovine samples has become necessary, as infected animals are potentially capable of infecting humans (zoonotic tuberculosis) (6). Besides M. bovis, transmission of M. tuberculosis from infected humans to animals and back has been reported (reverse zoonosis) (10,12,41). Hence, M. bovis and M. tuberculosis pose a potential health hazard to both animals and humans (1,15,43).The identification of the closely related members of the Mycobacterium tuberculosis complex (MTC) has remained a challenging task in diagnostic laboratories (7,30,44). MTC includes a variety of closely related mycobacteria, namely, M. tuberculosis, M. bovis, M. canetti, M. africanum, and M. microti. A panel of classical tests based on microbiological features such as growth rate and phenotypic and biochemical characteristics has conventionally been utilized to distinguish members of MTC (30). However, these tests are slow, cumbersome, unreliable, and time-consuming. The high degree of variability among these tests warrants the development of molecular biological tools for identification of MTC members. In this regard, multiple gene targets have been used to date to detect and differentiate genetically identical species, such as M. tuberculosis and M. bovis. The gene targets include pncA (2,29,36), gyrB (5), oxyR (42), and katG (19). Huard et al. (21) and Richter et al. (33) have targeted multiple loci and genes to differentiate M. tuberculosis from M. bovis. However, to date no single accepted protocol(s) that can unambiguously differentiate all members of the MTC is available. Identification of the etiological agent belonging to MTC is important for determination of the origin and reservoirs of infection and also for implementation of appropriate public health measures.Our laboratory earlier described a PCR-restriction fragment length polymorphism (RFLP) method utilizing the hupB gene,